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Method: Genome-scale coestimation of species and gene trees
- Bastien Boussau,
- Gergely J. Szöllősi,
- Laurent Duret,
- Manolo Gouy,
- Eric Tannier,
- and Vincent Daubin
Genome Res. February 2013 23: 323-330; Published in Advance November 6, 2012, doi:10.1101/gr.141978.112
...the correct model of evolution. For PHYLDOG, the median RF distance to the true tree is at 0. Figure 3. Mammalian tree reconstructed by PHYLDOG, with arbitrary branch lengths. Ancestral gene contents obtained using PhyML (red), TreeBeST (green), and PHYLDOG (blue) are shown for several nodes (circled). Genome-scale...
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Resource: Genome-scale phylogenetic function annotation of large and diverse protein families
- Barbara E. Engelhardt,
- Michael I. Jordan,
- John R. Srouji,
- and Steven E. Brenner
Genome Res. November 2011 21: 1969-1980; Published in Advance July 22, 2011, doi:10.1101/gr.104687.109
...functions and on the limitations of the Gene Ontology. As such, we do not have a precision-recall analysis because we rebuilt the GeneOntology for this family and because the BLAST keyword script did not include all ancestral terms of the candidate functions, which is prohibitively time-consuming to build...
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Methods: Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
...– 2423 . ↵ Bourque, G. , Pevzner, P.A. ( 2002 ) Genome-scale evolution: Reconstructing gene orders in the ancestral species . Genome Res. 12 : 26 – 36 . ↵ Bourque, G. , Tesler, G. , Pevzner, P.A. ( 2006 ) The convergence of cytogenetics and rearrangement-based models for ancestral reconstruction . Genome...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...36: 518–522. Bourque G, Pevzner PA. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 12: 26–36. Carvalho AB, Koerich LB, Clark AG. 2009. Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet 25: 270–277. Chang TC, Klabnik JL, LiuWS. 2011...
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Resource: The pig X and Y Chromosomes: structure, sequence, and evolution
- Benjamin M. Skinner,
- Carole A. Sargent,
- Carol Churcher,
- Toby Hunt,
- Javier Herrero,
- Jane E. Loveland,
- Matt Dunn,
- Sandra Louzada,
- Beiyuan Fu,
- William Chow,
- James Gilbert,
- Siobhan Austin-Guest,
- Kathryn Beal,
- Denise Carvalho-Silva,
- William Cheng,
- Daria Gordon,
- Darren Grafham,
- Matt Hardy,
- Jo Harley,
- Heidi Hauser,
- Philip Howden,
- Kerstin Howe,
- Kim Lachani,
- Peter J.I. Ellis,
- Daniel Kelly,
- Giselle Kerry,
- James Kerwin,
- Bee Ling Ng,
- Glen Threadgold,
- Thomas Wileman,
- Jonathan M.D. Wood,
- Fengtang Yang,
- Jen Harrow,
- Nabeel A. Affara,
- and Chris Tyler-Smith
Genome Res. January 2016 26: 130-139; Published in Advance November 11, 2015, doi:10.1101/gr.188839.114
...on the short and long arms. Comparative chromosome organization and gene order between mammals Previous work fromprimates, mouse, cat, and dog has reconstructed a putative ancestral eutherian Y Chromosome (Li et al. 2013a) based on gene order. We incorporated our pig gene order into this and added information...
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ARTICLE: Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes
- Guillaume Bourque,
- Pavel A. Pevzner,
- and Glenn Tesler
Genome Res. April 2004 14: 507-516; doi:10.1101/gr.1975204
...informatics workshop (eds. S. Miyano and T. Takagi), pp. 25 -34. University Academy Press, Tokyo, Japan. ↵ Bourque, G. and Pevzner, P.A. 2002 . Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res. 12 : 9748 -9753. ↵ Caprara, A. 2003 . The reversal median problem. INFORMS J...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
...completed whole-genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm MGRA for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee...
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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...diversity. They anticorrelate at the genomic scale, so that protein families with many paralogs tend to have fewer transcript variants and vice versa (Talavera et al. 2007). It is therefore expected that some genes shifted from one strategy to the other during evolution: The function of an alternative...
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Method: Quantification of GC-biased gene conversion in the human genome
- Sylvain Glémin,
- Peter F. Arndt,
- Philipp W. Messer,
- Dmitri Petrov,
- Nicolas Galtier,
- and Laurent Duret
Genome Res. August 2015 25: 1215-1228; Published in Advance May 20, 2015, doi:10.1101/gr.185488.114
...Quantification of GC-biased gene conversion in the human Sylvain Glémin1,2, Peter F. Arndt3, Philipp W. Messer4, Dmitri Petrov5, Nicolas Galtier1 and Laurent Duret6 1Institut des Sciences de l'Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE), 34095 Montpellier, France; 2...
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LETTER: The net of life: Reconstructing the microbial phylogenetic network
- Victor Kunin,
- Leon Goldovsky,
- Nikos Darzentas,
- and Christos A. Ouzounis
Genome Res. July 2005 15: 954-959; Published in Advance June 17, 2005, doi:10.1101/gr.3666505
...Genet. 18 : 158 -162. ↵ Kunin, V. and Ouzounis, C.A. 2003a . The balance of driving forces during evolution in prokaryotes. Genome Res. 13 : 1589 -1594. ↵ ———. 2003b . GeneTRACE: Reconstruction of gene content of ancestral species. Bioinformatics 19 : 1412 -1416. ↵ Kunin, V., Ahren, D., Goldovsky, L...

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